David Cameron has said he is prepared to give the defence secretary, Liam Fox, time to answer allegations about his links with his friend Adam Werritty.

He said Fox had his support whilst he answered those questions and added that he would not make a judgment to suit newspaper deadlines.

Downing Street is to wait for an interim report from the Ministry of Defence permanent secretary, Ursula Brennan, later on Monday before deciding whether to refer the defence secretary to Sir Philip Mawer, the independent adviser on ministerial standards, to decide whether there has been a breach of the ministerial code.

Fox will answer questions in the Commons later, first at defence questions and then in a statement.

Cameron told Sky News: "It is very important, in politics and in life, to be scrupulously fair. He is an excellent defence secretary. He is answering these questions and allegations in the right way and in the right time.

"I do not run these things according to newspaper deadlines or press pressure. Let us get the answer to these questions and then let's move ahead with Liam going to do a very good job. Liam last night said very clearly areas where he had made mistakes and … expressed regret and he said he was sorry."

Downing Street said it was determined to establish the full facts, but it is clear that the cabinet secretary, Sir Gus O'Donnell, is taking a grip on the situation.

Downing Street refused to say whether it had been told in advance that Fox was setting up an internal two-week inquiry into his links with Werritty.

If Fox had consulted No 10 in advance on Friday, it is almost certain that Cameron's spokesman would have said so. The spokesman avoided the issue by saying he was not going to get into process.

The prime minister faces a choice between waiting for a full report by Brennan – not due until October 21 – or passing the case to Mawer in the next 24 hours to determine whether there has been a breach.

It is clear that Cameron does not wish to lose his defence secretary, but he is also aware of the potential damage to his government if he is seen to be the judge and jury on whether Fox's position as defence secretary has been compromised by his loyalty to Werritty.

At a regular daily briefing in Westminster, Cameron's spokesman said: "There has been a series of allegations made. Before we draw any conclusions we want to establish the facts – and not just some of the facts, but the full picture."

He stressed that Monday's report represented only the "interim findings" of an inquiry and, asked whether Cameron had full confidence in Fox, said: "Absolutely."

The spokesman added: "The prime minister thinks that Liam Fox has been doing an excellent job as secretary of state. He inherited a department which was in a real mess, and he has made great strides in tackling that."